This article discusses the Brazilian National Policy for Indigenous People's Health, formulated in the 1990s as part of the national Health Reform Movement and based on the creation (in 1999) of the Indigenous Healthcare Sub-System. Coordinated at the central government level under the administration of the National Health Foundation/Ministry of Health, the implementation of this sub-system required adaptations in the organization of health services systems at the local level, with the creation of Special Indigenous Health Districts. This configuration showed the need for dialogue and negotiation among the various institutions involved with indigenous affairs, from the perspective of overcoming various conflicts and operational difficulties. The current analysis identifies the difficulties in the implementation of a differentiated indigenous health policy under federal responsibility and within the decentralized Brazilian Unified Health System (SUS), since the absence of specific mechanisms and instruments regulating the operationalization of these services at the local level and the lack of more effective supervision and on-going evaluation of this policy mean that differentiated care for the indigenous population is subject to both the vices and virtues of local policy.